unit tests

src/main/java/org/cidarlab/eugene/data/sbol/mapping/Eugene2SBOL.java

@@ -581,7 +581,7 @@ private static URI soMapping(String s) {
         }
 
         // Update Lookup Table
-        _logicLayer.AddOrUpdateSO(retVal, s);
+        _logicLayer.AddOrUpdateSO(retVal.toString(), s);
         return retVal;
     }
 

src/main/java/org/cidarlab/eugene/data/sbol/mapping/sbolConversionAPI/MongoConnection.java

@@ -2,8 +2,11 @@
 
 import com.mongodb.MongoClient;
 import com.mongodb.MongoClientURI;
+import com.mongodb.MongoCredential;
 import com.mongodb.client.MongoCollection;
+import com.mongodb.client.MongoCursor;
 import com.mongodb.client.MongoDatabase;
+import com.mongodb.client.MongoIterable;
 import org.bson.Document;
 
 /**
@@ -24,24 +27,28 @@ public MongoCollection getCollection(String colName) {
         return collection;
     }
 
+    public MongoIterable<String> getCollectionNames() {
+//        Document retVal = db.runCommand(new Document("listCollections", 1));
+        MongoIterable<String> retVal = db.listCollectionNames();
+
+        return retVal;
+    }
+
     public void login(String user, String pw) throws Exception {
         if (user == null || pw == null) {
         }
+        // To connect to mongodb server
+        String uri = String.format("mongodb://%s:%[email protected]:53412/lookuptables", user, pw);
+
+        MongoCredential mongoCredential = MongoCredential.createScramSha1Credential("admin", "admin",
+          "admin123".toCharArray());
+        MongoClientURI connectionString = new MongoClientURI(uri);
+        client = new MongoClient(connectionString);
+        db = client.getDatabase("lookuptables");
+        System.out.println("Connected to database successfully!");
+        //boolean auth = db.authenticate(myUserName, myPassword);
+        //System.out.println("Authentication: "+auth);
 
-        try {
-
-            // To connect to mongodb server
-            String uri = String.format("mongodb://%s:%[email protected]:53412/lookuptables", user, pw);
-            MongoClientURI connectionString = new MongoClientURI(uri);
-            client = new MongoClient(connectionString);
-            db = client.getDatabase("lookuptables");
-            System.out.println("Connect to database successfully");
-            //boolean auth = db.authenticate(myUserName, myPassword);
-            //System.out.println("Authentication: "+auth);
-
-        } catch (Exception e) {
-            System.err.println(e.getClass().getName() + ": " + e.getMessage());
-        }
     }
 
     public void logout() {

src/main/java/org/cidarlab/eugene/data/sbol/mapping/sbolConversionAPI/SBOLConversionDataLayer.java

@@ -31,6 +31,7 @@ public class SBOLConversionDataLayer {
     private Document doc;
 
     public SBOLConversionDataLayer() {
+        setUp();
     }
 
     public ArrayList<String> getEugenePartNames(String so) {
@@ -43,42 +44,51 @@ public ArrayList<String> getEugenePartNames(String so) {
         return names;
     }
 
-    public boolean insertEugenePartName(String so, String name) {
+    public void UpsertEugenePartName(String so, String name) {
+        if (findDocument(so)) {
+            updateSOTerm(so, name, true);
+            return;
+        }
 
         Document d = new Document("sequenceOntologyNumber", so)
           .append("eugenePartNames", Arrays.asList(name));
 
         collection.insertOne(d);
-
-        return true;
     }
 
     public boolean removeEugenePartName(String so, String name) {
         boolean retVal = true;
 
+        if (findDocument(so)) {
+            updateSOTerm(so, name, false);
+        }
+
         return retVal;
     }
 
-    public boolean updateSOTerm(String so, String name) {
+    private void updateSOTerm(String so, String name, boolean addName) {
         ArrayList<String> names = (ArrayList) doc.get("eugenePartNames");
 
-        names.add(name);
+        if (addName == names.contains(name)) {
+            return;
+        }
 
-        doc.put("eugenePartNames", names);
+        if (addName) {
+            names.add(name);
+        } else {
+            names.remove(name);
+        }
 
-        // TO DO: Don't replace whole doc, just update it.
-        collection.updateOne(
-          eq("sequenceOntologyNumber", so),
-          doc);
-        return true;
+        collection.updateOne(eq("sequenceOntologyNumber", so),
+          new Document("$set", new Document("eugenePartNames", names)));
     }
 
     private boolean findDocument(String so) {
-        boolean retVal = true;
 
         doc = (Document) collection.find(eq("sequenceOntologyNumber", so)).first();
 
-        //if doc something
+        boolean retVal = doc != null;
+
         return retVal;
     }
 
@@ -87,7 +97,7 @@ private void setUp() {
         _instance = new MongoConnection();
 
         try {
-            _instance.login("shamseen@bu.edu", "lcp");
+            _instance.login("shamseen", "lcp");
             collection = _instance.getCollection("SBOL2Conversions");
 
         } catch (Exception e) {

src/main/java/org/cidarlab/eugene/data/sbol/mapping/sbolConversionAPI/SBOLConversionLogicLayer.java

@@ -18,42 +18,50 @@ public class SBOLConversionLogicLayer {
     private SBOLConversionDataLayer _dataLayer;
     private List<String> names;
     private int uriIndex;
+    private String _so;
 
     // TO DO: Error handling
     public SBOLConversionLogicLayer() {
         _dataLayer = new SBOLConversionDataLayer();
-        uriIndex = SequenceOntology.NAMESPACE.toString().length();
+        String uri = SequenceOntology.NAMESPACE.toString() + "SO_";
+        uriIndex = uri.length();
     }
 
-    public void AddOrUpdateSO(URI so, String name) {
-        insertOrUpdate(so, name);
+    public void AddOrUpdateSO(String so, String name) {
+        takeSONumberFromURI(so);
+        insertOrUpdate(name);
     }
 
     public boolean DeleteEugenePartName(String so, String name) {
-        return deleteEugenePartName(so, name);
+        takeSONumberFromURI(so);
+        return deleteEugenePartName(name);
     }
 
     public List<String> GetEugeneNames(String so) {
-        getEugeneNames(so);
+        takeSONumberFromURI(so);
+        getEugeneNames();
         return names;
     }
 
-    private boolean deleteEugenePartName(String so, String name) {
-        boolean retVal = _dataLayer.removeEugenePartName(so, name);
+    private boolean deleteEugenePartName(String name) {
+        boolean retVal = _dataLayer.removeEugenePartName(_so, name);
         return retVal;
     }
 
-    private void getEugeneNames(String so) {
-        names = _dataLayer.getEugenePartNames(so);
+    private void getEugeneNames() {
+        names = _dataLayer.getEugenePartNames(_so);
     }
 
-    private void insertOrUpdate(URI _so, String name) {
-        String so = _so.toString().substring(uriIndex);
+    private void insertOrUpdate(String name) {
+        _dataLayer.UpsertEugenePartName(_so, name);
+    }
 
-        getEugeneNames(so);
-        if (names.isEmpty()) {
-            _dataLayer.insertEugenePartName(so, name);
+    private void takeSONumberFromURI(String so) {
+        if (so.length() > uriIndex) {
+            so = so.substring(uriIndex);
         }
+
+        _so = so;
     }
 
 }